J. Comput. Biol. - Parallel continuous flow: a parallel suffix tree construction tool for whole genomes.

Tópicos

{ sequenc(1873) structur(1644) protein(1328) }
{ structur(1116) can(940) graph(676) }
{ algorithm(1844) comput(1787) effici(935) }
{ perform(999) metric(946) measur(919) }
{ gene(2352) biolog(1181) express(1162) }
{ studi(2440) review(1878) systemat(933) }
{ assess(1506) score(1403) qualiti(1306) }
{ general(901) number(790) one(736) }
{ search(2224) databas(1162) retriev(909) }
{ research(1085) discuss(1038) issu(1018) }
{ import(1318) role(1303) understand(862) }
{ data(3008) multipl(1320) sourc(1022) }
{ system(1976) rule(880) can(841) }
{ network(2748) neural(1063) input(814) }
{ take(945) account(800) differ(722) }
{ problem(2511) optim(1539) algorithm(950) }
{ chang(1828) time(1643) increas(1301) }
{ method(1557) propos(1049) approach(1037) }
{ data(1714) softwar(1251) tool(1186) }
{ care(1570) inform(1187) nurs(1089) }
{ model(2341) predict(2261) use(1141) }
{ blood(1257) pressur(1144) flow(957) }
{ spatial(1525) area(1432) region(1030) }
{ group(2977) signific(1463) compar(1072) }
{ time(1939) patient(1703) rate(768) }
{ cancer(2502) breast(956) screen(824) }
{ use(976) code(926) identifi(902) }
{ result(1111) use(1088) new(759) }
{ implement(1333) system(1263) develop(1122) }
{ model(3404) distribut(989) bayesian(671) }
{ can(774) often(719) complex(702) }
{ imag(1947) propos(1133) code(1026) }
{ data(1737) use(1416) pattern(1282) }
{ inform(2794) health(2639) internet(1427) }
{ measur(2081) correl(1212) valu(896) }
{ imag(1057) registr(996) error(939) }
{ bind(1733) structur(1185) ligand(1036) }
{ method(1219) similar(1157) match(930) }
{ featur(3375) classif(2383) classifi(1994) }
{ imag(2830) propos(1344) filter(1198) }
{ imag(2675) segment(2577) method(1081) }
{ patient(2315) diseas(1263) diabet(1191) }
{ motion(1329) object(1292) video(1091) }
{ treatment(1704) effect(941) patient(846) }
{ surgeri(1148) surgic(1085) robot(1054) }
{ framework(1458) process(801) describ(734) }
{ error(1145) method(1030) estim(1020) }
{ learn(2355) train(1041) set(1003) }
{ concept(1167) ontolog(924) domain(897) }
{ clinic(1479) use(1117) guidelin(835) }
{ extract(1171) text(1153) clinic(932) }
{ design(1359) user(1324) use(1319) }
{ control(1307) perform(991) simul(935) }
{ model(2220) cell(1177) simul(1124) }
{ method(984) reconstruct(947) comput(926) }
{ featur(1941) imag(1645) propos(1176) }
{ case(1353) use(1143) diagnosi(1136) }
{ howev(809) still(633) remain(590) }
{ data(3963) clinic(1234) research(1004) }
{ studi(1410) differ(1259) use(1210) }
{ risk(3053) factor(974) diseas(938) }
{ system(1050) medic(1026) inform(1018) }
{ visual(1396) interact(850) tool(830) }
{ compound(1573) activ(1297) structur(1058) }
{ perform(1367) use(1326) method(1137) }
{ studi(1119) effect(1106) posit(819) }
{ record(1888) medic(1808) patient(1693) }
{ health(3367) inform(1360) care(1135) }
{ model(3480) simul(1196) paramet(876) }
{ monitor(1329) mobil(1314) devic(1160) }
{ ehr(2073) health(1662) electron(1139) }
{ state(1844) use(1261) util(961) }
{ research(1218) medic(880) student(794) }
{ patient(2837) hospit(1953) medic(668) }
{ model(2656) set(1616) predict(1553) }
{ data(2317) use(1299) case(1017) }
{ age(1611) year(1155) adult(843) }
{ medic(1828) order(1363) alert(1069) }
{ signal(2180) analysi(812) frequenc(800) }
{ cost(1906) reduc(1198) effect(832) }
{ sampl(1606) size(1419) use(1276) }
{ first(2504) two(1366) second(1323) }
{ intervent(3218) particip(2042) group(1664) }
{ activ(1138) subject(705) human(624) }
{ patient(1821) servic(1111) care(1106) }
{ use(2086) technolog(871) perceiv(783) }
{ can(981) present(881) function(850) }
{ analysi(2126) use(1163) compon(1037) }
{ health(1844) social(1437) communiti(874) }
{ high(1669) rate(1365) level(1280) }
{ use(1733) differ(960) four(931) }
{ drug(1928) target(777) effect(648) }
{ survey(1388) particip(1329) question(1065) }
{ estim(2440) model(1874) function(577) }
{ decis(3086) make(1611) patient(1517) }
{ process(1125) use(805) approach(778) }
{ activ(1452) weight(1219) physic(1104) }
{ method(1969) cluster(1462) data(1082) }
{ method(2212) result(1239) propos(1039) }
{ detect(2391) sensit(1101) algorithm(908) }

Resumo

The construction of suffix trees for very long sequences is essential for many applications, and it plays a central role in the bioinformatic domain. With the advent of modern sequencing technologies, biological sequence databases have grown dramatically. Also the methodologies required to analyze these data have become more complex everyday, requiring fast queries to multiple genomes. In this article, we present parallel continuous flow (PCF), a parallel suffix tree construction method that is suitable for very long genomes. We tested our method for the suffix tree construction of the entire human genome, about 3GB. We showed that PCF can scale gracefully as the size of the input genome grows. Our method can work with an efficiency of 90% with 36 processors and 55% with 172 processors. We can index the human genome in 7 minutes using 172 processes.

Resumo Limpo

construct suffix tree long sequenc essenti mani applic play central role bioinformat domain advent modern sequenc technolog biolog sequenc databas grown dramat also methodolog requir analyz data becom complex everyday requir fast queri multipl genom articl present parallel continu flow pcf parallel suffix tree construct method suitabl long genom test method suffix tree construct entir human genom gb show pcf can scale grace size input genom grow method can work effici processor processor can index human genom minut use process

Resumos Similares

J Chem Inf Model - Protein secondary structure classification revisited: processing DSSP information with PSSC. ( 0,792882925340723 )
Comput Biol Chem - Identification of putative and potential cross-reactive chickpea (Cicer arietinum) allergens through an in silico approach. ( 0,788561169031633 )
Comput Biol Chem - Subgrouping Automata: automatic sequence subgrouping using phylogenetic tree-based optimum subgrouping algorithm. ( 0,77037683352353 )
Comput Math Methods Med - DV-curve representation of protein sequences and its application. ( 0,766120786130398 )
J Chem Inf Model - Parallel and antiparallel ?-strands differ in amino acid composition and availability of short constituent sequences. ( 0,76390095927422 )
J. Comput. Biol. - Detection of structural variants involving repetitive regions in the reference genome. ( 0,76045232045526 )
J Biomed Inform - A similarity network approach for the analysis and comparison of protein sequence/structure sets. ( 0,742490021783558 )
Comput Biol Chem - A novel feature representation method based on Chou's pseudo amino acid composition for protein structural class prediction. ( 0,739276964576849 )
J Chem Inf Model - Comparative analysis of threshold and tessellation methods for determining protein contacts. ( 0,734017135218222 )
J. Comput. Biol. - A theoretical model for whole genome alignment. ( 0,733540917062186 )
J Chem Inf Model - Beyond terrestrial biology: charting the chemical universe of a-amino acid structures. ( 0,729707100000153 )
J. Comput. Biol. - Statistical significance of optical map alignments. ( 0,724922187404837 )
Comput Biol Chem - Large replication skew domains delimit GC-poor gene deserts in human. ( 0,71305686581782 )
J. Comput. Biol. - Pathset graphs: a novel approach for comprehensive utilization of paired reads in genome assembly. ( 0,712347500198436 )
Comput Biol Chem - Tracing the evolution of the mitochondrial protein import machinery. ( 0,711712196090289 )
J. Comput. Biol. - ComB: SNP calling and mapping analysis for color and nucleotide space platforms. ( 0,709140360047622 )
Brief. Bioinformatics - Computational methods for Gene Orthology inference. ( 0,706591329886423 )
Comput. Biol. Med. - A protein mapping method based on physicochemical properties and dimension reduction. ( 0,7061878636038 )
J. Comput. Biol. - Combinatorics of -structures. ( 0,705060667572256 )
Comput Biol Chem - Exploring the limits of fold discrimination by structural alignment: a large scale benchmark using decoys of known fold. ( 0,704378514323656 )
Comput Methods Programs Biomed - Pinda: a web service for detection and analysis of intraspecies gene duplication events. ( 0,70425044468953 )
J Chem Inf Model - Modules identification in protein structures: the topological and geometrical solutions. ( 0,6979026509178 )
Comput Biol Chem - ProCoCoA: A quantitative approach for analyzing protein core composition. ( 0,691347512383906 )
Brief. Bioinformatics - Ultrafast clustering algorithms for metagenomic sequence analysis. ( 0,68764207002527 )
J. Comput. Biol. - IDBA-MTP: A Hybrid Metatranscriptomic Assembler Based on Protein Information. ( 0,683349790839467 )
J. Comput. Biol. - Evaluating, comparing, and interpreting protein domain hierarchies. ( 0,683014726727381 )
Comput Biol Chem - The frequency of poly(G) tracts in the human genome and their use as a sensor of DNA damage. ( 0,682952933113953 )
J. Comput. Biol. - Simultaneous alignment and folding of protein sequences. ( 0,681389681883732 )
Comput. Biol. Med. - An insight into the molecular basis for convergent evolution in fish antifreeze Proteins. ( 0,681297039049885 )
IEEE Trans Vis Comput Graph - Output-Sensitive Construction of Reeb Graphs. ( 0,678083373771348 )
IEEE Trans Image Process - Complex object correspondence construction in two-dimensional animation. ( 0,676591597387041 )
J. Comput. Biol. - Shapes of RNA pseudoknot structures. ( 0,676198725278483 )
Brief. Bioinformatics - Base-calling for next-generation sequencing platforms. ( 0,675282528654854 )
J Chem Inf Model - Searching for likeness in a database of macromolecular complexes. ( 0,672759882968051 )
J. Comput. Biol. - Random matrix approach to the distribution of genomic distance. ( 0,672440625656673 )
Comput Biol Chem - Analysis of sequence repeats of proteins in the PDB. ( 0,670247689262595 )
Comput Biol Chem - Computational determination of the orientation of a heat repeat-like domain of DNA-PKcs. ( 0,668568715229876 )
Comput. Biol. Med. - Improving protein complex classification accuracy using amino acid composition profile. ( 0,667597788264667 )
J. Comput. Biol. - A Bayesian sampler for optimization of protein domain hierarchies. ( 0,665993219137561 )
J. Comput. Biol. - Sequence alignment of viral channel proteins with cellular ion channels. ( 0,665944353943284 )
BMC Med Inform Decis Mak - Efficient protein structure search using indexing methods. ( 0,665208382645183 )
Comput Biol Chem - Protein folding simulations of 2D HP model by the genetic algorithm based on optimal secondary structures. ( 0,664670869812418 )
J Chem Inf Model - ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures. ( 0,660592007231516 )
Brief. Bioinformatics - De novo assembly of short sequence reads. ( 0,660403581964486 )
Comput Biol Chem - Characterizing regions in the human genome unmappable by next-generation-sequencing at the read length of 1000 bases. ( 0,65818616517953 )
Comput Biol Chem - Bacterial protein structures reveal phylum dependent divergence. ( 0,656865313710762 )
J. Comput. Biol. - Optimization of profile-to-profile alignment parameters for one-dimensional threading. ( 0,654738928723668 )
Comput Methods Programs Biomed - Can computational biology improve the phylogenetic analysis of insulin? ( 0,653952723075453 )
J. Comput. Biol. - Statistical significance of threading scores. ( 0,652821389035003 )
J. Comput. Biol. - Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. ( 0,652268767805531 )
Comput Math Methods Med - ADLD: a novel graphical representation of protein sequences and its application. ( 0,651929463218242 )
Brief. Bioinformatics - Ortholog identification in the presence of domain architecture rearrangement. ( 0,651577336507253 )
J Chem Inf Model - Protein secondary structure prediction with SPARROW. ( 0,64979837606336 )
Comput Biol Chem - An efficient similarity search based on indexing in large DNA databases. ( 0,648674973140802 )
Brief. Bioinformatics - Systematic identification of Class I HDAC substrates. ( 0,64755562222285 )
Comput Biol Chem - Identical sequence patterns in the ends of exons and introns of human protein-coding genes. ( 0,647361212405455 )
Comput Methods Programs Biomed - Protein secondary structure prediction using modular reciprocal bidirectional recurrent neural networks. ( 0,646992471273795 )
Brief. Bioinformatics - Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. ( 0,646671312113858 )
Artif Intell Med - Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle. ( 0,646612358659324 )
IEEE Trans Vis Comput Graph - Dynamic Network Visualization with Extended Massive Sequence Views. ( 0,64655439292612 )
Comput Biol Chem - A degree-distribution based hierarchical agglomerative clustering algorithm for protein complexes identification. ( 0,645992110942655 )
J Integr Bioinform - Complementarity of network and sequence information in homologous proteins. ( 0,645942839411976 )
J. Comput. Biol. - AREM: aligning short reads from ChIP-sequencing by expectation maximization. ( 0,644792661060574 )
Brief. Bioinformatics - Application of second-generation sequencing to cancer genomics. ( 0,644343826985321 )
J. Comput. Biol. - Reconstructing the history of large-scale genomic changes: biological questions and computational challenges. ( 0,643090476589625 )
J. Comput. Biol. - Efficient traversal of beta-sheet protein folding pathways using ensemble models. ( 0,640714688845252 )
Comput Biol Chem - Statistical analysis and exposure status classification of transmembrane beta barrel residues. ( 0,640478279299466 )
J. Comput. Biol. - Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. ( 0,637564589460463 )
Comput Biol Chem - Identification and characterization of lysine-methylated sites on histones and non-histone proteins. ( 0,637289905388454 )
Comput. Biol. Med. - A content and structural assessment of oxidative motifs across a diverse set of life forms. ( 0,636574615845213 )
Brief. Bioinformatics - A practical guide for the computational selection of residues to be experimentally characterized in protein families. ( 0,636555714106217 )
Brief. Bioinformatics - New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. ( 0,636115198201777 )
Comput Biol Chem - ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures. ( 0,634742411154134 )
Comput Biol Chem - Investigating long range correlation in DNA sequences using significance tests of conditional mutual information. ( 0,634573343289915 )
Brief. Bioinformatics - BamView: visualizing and interpretation of next-generation sequencing read alignments. ( 0,632982938471657 )
Comput Biol Chem - Protein fold recognition based on functional domain composition. ( 0,631732257954069 )
J Chem Inf Model - Tertiary structure prediction of RNA-RNA complexes using a secondary structure and fragment-based method. ( 0,630114430967871 )
Comput Biol Chem - Computational insight into nitration of human myoglobin. ( 0,62984064561251 )
Curr Protoc Bioinformatics - Using the RNAstructure Software Package to Predict Conserved RNA Structures. ( 0,62946018324447 )
Comput Biol Chem - Human-chimpanzee alignment: ortholog exponentials and paralog power laws. ( 0,627258081769385 )
Comput. Biol. Med. - miRClassify: an advanced web server for miRNA family classification and annotation. ( 0,627004190002548 )
J Integr Bioinform - Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. ( 0,625687194133128 )
J. Comput. Biol. - Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs. ( 0,625003698821868 )
J. Comput. Biol. - Computational techniques for human genome resequencing using mated gapped reads. ( 0,624960476544128 )
J. Comput. Biol. - Emergent protein folding modeled with evolved neural cellular automata using the 3D HP model. ( 0,623899816939036 )
IEEE Trans Image Process - Hyperspectral image representation and processing with binary partition trees. ( 0,623879466904938 )
Comput Math Methods Med - Quad-PRE: a hybrid method to predict protein quaternary structure attributes. ( 0,623412811163701 )
Comput Math Methods Med - Coarse-grained simulation of myosin-V movement. ( 0,623123445460711 )
J. Comput. Biol. - Nonparametric combinatorial sequence models. ( 0,622969206920763 )
Comput Biol Chem - A local average connectivity-based method for identifying essential proteins from the network level. ( 0,622465883316932 )
J Chem Inf Model - Building a knowledge-based statistical potential by capturing high-order inter-residue interactions and its applications in protein secondary structure assessment. ( 0,622399777913784 )
IEEE Trans Pattern Anal Mach Intell - The Sum-over-Forests Density Index: Identifying Dense Regions in a Graph. ( 0,622188396773389 )
Brief. Bioinformatics - Taxonomic binning of metagenome samples generated by next-generation sequencing technologies. ( 0,621923360133365 )
Comput. Biol. Med. - Improving protein secondary structure prediction using a multi-modal BP method. ( 0,615997291616408 )
Comput Biol Chem - A novel empirical mutual information approach to identify co-evolving amino acid positions of influenza A viruses. ( 0,613737978363789 )
Sci Data - Genomes of diverse isolates of the marine cyanobacterium Prochlorococcus. ( 0,613641517191305 )
Comput Biol Chem - Molecular phylogenetic study and expression analysis of ATP-binding cassette transporter gene family in Oryza sativa in response to salt stress. ( 0,612940235943595 )
Comput Biol Chem - Multi-nucleation and vectorial folding pathways of large helix protein. ( 0,612775211320581 )
J. Comput. Biol. - Ray: simultaneous assembly of reads from a mix of high-throughput sequencing technologies. ( 0,612147822484153 )
Sci Data - Comprehensive analysis of the venom gland transcriptome of the spider Dolomedes fimbriatus. ( 0,611734639449974 )